ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.2157G>A (p.Ala719=) (rs201523530)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000724450 SCV000226204 uncertain significance not provided 2015-01-15 criteria provided, single submitter clinical testing
GeneDx RCV000174829 SCV000534757 likely benign not specified 2016-12-13 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV001087616 SCV000752104 likely benign Glycogen storage disease, type II 2020-11-21 criteria provided, single submitter clinical testing
Broad Institute Rare Disease Group, Broad Institute RCV001087616 SCV001422768 likely benign Glycogen storage disease, type II 2020-01-22 no assertion criteria provided curation The c.2157G>A (p.Ala719=) variant in GAA has not been previously reported in individuals with Glycogen Storage Disease II but has been reported in 1 European individual with unexplained limb-girdle muscle weakness (PMID: 29149851). This variant has also been reported as a VUS by EGL and a likely benign variant by GeneDx and Invitae in ClinVar (Variation ID: 194459). This variant has been identified in 0.05516% (18/32630) of Latino chromosomes and 0.01804% (4/22168) of African chromosomes by the Genome Aggregation Database (gnomAD,; dbSNP rs201523530). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. Computational prediction tools and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. However, novel synonymous variants supported by computational evidence without raised suspicion for an impact are likely benign (Richards 2015). In summary, although additional studies are required to fully establish its clinical significance, this variant is likely benign. ACMG/AMP Criteria applied: PM2, BP4, BP7 (Richards 2015).

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